Background Late stent thrombosis (LST) is still conced by interventions cardiologists in daily clinical practice. This study aimed to compare the incidence of LST after implantation of different drug-eluting stents (DES) in coronary heart disease (CHD) patients in the real world.Methods From December 2001 to February 2009, a total of 11 875 consecutive CHD patients undergone DES implantation were enrolled in this single-center registery study. Patients with acute ST-segment elevation myocardial infarction, mixed DES implantation, restenosis lesions, and patients who could not take dual antiplatlet medication and those who were contraindicated for coronary interventional treatment were excluded. All patients were treated with completed dual antiplatelet medications for at least 9 months after DES deployment. The follow-up was completed by outpatient visits, letter correspondence, phone calls and coronary angiography. Definite LST was diagnosed auording to the Academic Research Consortium (ARC) definition.Results Cypher or Cypher Select stents were implanted in 4104 cases, Taxus or Taxus Liberty stents in 2271 cases and Firebird stents (Chinese rapamycin-eluting stents) in 5500 cases. One-year follow-up was completed in 9693 patients, including 3346 cases with Cypher or Cypher Select stents, 1529 cases with Taxus or Taxus Liberty stents and 4818 cases with Firebird stents. Two- and three-year follow-up results were obtained in 7133 and 4353 patients, respectively, including 2410 and 1760 cases with Cypher or Cypher Select stents, 1285 and 900 cases with Taxus or Taxus Liberty stents as well as 3438 and 1693 cases with Firebird stents. One-year follow-up results showed that the incidence of LST was 1.08% in patients with Cypher or Cypher Select stents, 1.24% in those with Taxus or Taxus Liberty stents and 0.71% in those with Firebird stents; there was no significant difference between those with Cypher or Cypher Select and Firebird stents, but there was significant difference between those with Taxus or Taxus Liberty and Firebird stents (P=0.044). The incidence of LST at the 2- and 3-year follow-up was 1.33% and 1.70% in those with Cypher or Cypher Select stents, 1.40% and 1.70% in those with Taxus or Taxus Liberty stents, and 0.83% and 0.95% in those with Firebird stents, respectively. There were no significant differences among the three groups.Conclusions This study indicates that first-generation DES are acceptable to treat complex coronary lesions, and there is no significant difference of LST for three different DES.